Displacement polynucleotide assay method and polynucleotide complex reagent therefor
Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme
Methods for in-solution quenching of fluorescently labeled oligonucleotide probes
Method for detecting nucleic acid amplification using self-quenching fluorescence probe
Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to donor energy transfer system
Methods for in-solution quenching of fluorescently labeled oligonucleotide probes
Detection of nucleic acids using a hairpin forming oligonucleotide primer and an energy transfer detection system
Detection of nucleic acids using G-quartets
Methods for combined PCR amplification and hybridization probing using doubly labeled fluorescent probes
ApplicationNo. 12870737 filed on 08/27/2010
US Classes:435/91.1Polynucleotide (e.g., nucleic acid, oligonucleotide, etc.) , 435/6.12
ExaminersPrimary: Benzion, Gary
Assistant: Tung, Joyce
Attorney, Agent or Firm
Foreign Patent References
International ClassesC12Q 1/68
Description>SCOPE OF THE INVENTION
This invention relates to unequal length complementary probes which have a fluorophore on one probe and a quencher on the other. The fluorophore and quencher are juxtaposed in a manner such that the proximity of the quencher to the fluorophorequenches the fluorescence of the fluorphore. These probes are useful in detecting nucleotides with sequence complemenarity. The detection capabilities reside in the competitive hybridization resulting from the use of unequal length probes, and thesubsequent decrease in quenching brought about by this competitive hybridization.
AREA OF THE INVENTION
Nucleic acid amplification techniques have added to the collection of techniques by which very small quantities of a nucleotides can be enhanced to a concentration where they can be detected by some means. Several amplification techniques havebecome available. The most wide-spread technique is that of polymerase chain reaction, or PCR as it is now commonly called. While the amplification techniques increase the number of target nucleotide sequences available for detection, or recovery anduse, a sensitive method is needed to detect the amplification product. Also, amplification technologies benefit from real-time monitoring of the amplification process. Real-time monitoring can detect non-reactive amplification runs, or detectinefficiencies in the process. Quantification of oligonucleotide burden may also be possible with real-time monitoring if such monitoring can be done without interfering with the amplification reaction.
The procedure of this invention is based on the fluorescence energy transfer between a fluorophore labeled probe and a quencher labeled probe, with sequence complementarity to each other. The probes used are of unequal length favoring theannealing of one probe to the target nucleic acid sequence over annealing to its complementary probe. In the absence of nucleic acids with sequences complementary or identical to the probe sequences (target sequence), the two probes would anneal to eachother. When the two probes are annealed to each other, the proximity of the quencher to the fluorophore produces quenching of the fluorescence of the fluorophore. In the presence of nucleic acid with sequences complementary or identical to the probesequence, some of the fluorophore labeled probe will hybridize to the nucleic acid target with the complementary sequence and be separated from the quencher and yield increased (unquenched) fluorescence. This difference in fluorescence can be used forspecific detection of the presence of nucleic acids with the target sequences.
SUMMARY OF THE INVENTION
In a first aspect, this invention relates to a method for monitoring nucleic acid amplification comprising performing nucleic acid amplification on a target polynucleotide wherein the amplification is carried out using any method using a firstoligonucleotide probe and a second shorter oligonucleotide probe varying in length by at least about 2 base pairs; the first probe having a fluorophore; the second being complementary with the first probe and having a quencher molecule capable ofquenching the fluorescence of said fluorophore, the fluorophore and quencher being attached on their respective probes at positions which results in the quencher molecule quenching the fluorescence of the fluorophore when the probes are hybridized,wherein the longer probe binds preferentially to the target polynucleotide and when preferentially bound to the target polynucleotide the fluorescence intensity of the fluorophore is greater than the fluorescence intensity of the fluorophore whenhybridized to the second probe, and monitoring the fluorescence of the fluorophore, the generation of fluorescence corresponding to the occurrence of nucleic acid amplification.
It also relates to a method for detecting the presence of a target polynucleotide using the unequal length probes.
The annealed probes with fluorophore and quencher are also part of this invention.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates the fluorescence signal obtained from a PCR amplification of target HCV RNA using unequal length probes where the longer probe had fluorophore on the 5' terminal carbon, the shorter probe had a quencher on the 3' terminalcarbon and was prepared by deleting three base pairs from the 5' terminus of the longer probe.
DETAILED DESCRIPTION OF THE INVENTION
This invention is used in conjunction with the amplification of a target polynucleotide by any method. These amplification techniques include PCR, ligase chain reaction (LCR), gap LCR, transcription mediated amplification (TAM), nucleic acidsequence based amplification (NASBA), and strand displacement amplification (SDA).
PCR is of greatest interest. PCR is described in many references, such as Innis et at, editors, PCR Protocols (Academic Press, New York, 1989); Sambrook et at, Molecular Cloning, Second Edition (Cold Spring Harbor Laboratory, New York, 1989);and the like. The binding site of the oligonucleotide probe is located between the PCR primers used to amplify the target polynucleotide. The PCR may be carried out using any polymerase. Because the intensity of the fluorescence signal intensifies asmore replicates are made of the target polynucleotide, any polymerase which increased the number of target polynucleotides will work in this method. Preferably, PCR is carried out using a thermostable polymerase. The preferred enzyme is a Taq DNApolymerase, e.g. Amplitaq. (Perkin-Elmer, Norwalk, Conn.), or an equivalent thermostable DNA polymerase. The annealing temperature of the PCR will be about 5 degree-10 degree C. below the melting temperature of the oligonucleotide probes employed. Thepolymerase Pwo has also been used with success in this invention.
The term "oligonucleotide" as used herein includes linear oligomers of natural or modified monomers or linkages, including deoxyribonucleosides, ribonucleosides, and the like, capable of specifically binding to a target polynucleotide by way ofa regular pattern of monomer-to-monomer interactions, such as Watson-Crick type of base pairing, or the like. Usually monomers are linked by phosphodiester bonds or analogs thereof to form oligonucleotides ranging in size from a few monomeric units,e.g. 3-4, to several tens of monomeric units. Whenever an oligonucleotide is represented by a sequence of letters, such as "ATGCCTG," it will be understood that the nucleotides are in 5' to 3' order from left to right and that "A" denotesdeoxyadenosine, "C" denotes deoxycytidine, "G" denotes deoxyguanosine, and "T" denotes thymidine, unless otherwise noted. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoranilidate, phosphoramidate, and the like. Generally, oligonucleotide probes of the invention will have a sufficient number of phosphodiester linkages adjacent to its 5' end so that the 5' to 3' exonuclease activity employed can efficiently degrade the bound probe to separate the reporter andquencher molecules.
"Perfectly matched" in reference to a duplex means that the poly- or oligonucleotide strands making up the duplex form a double stranded structure with one other such that every nucleotide in each strand undergoes Watson-Crick base pairing witha nucleotide in the other strand. The term also comprehends the pairing of nucleoside analogs, such as deoxyinosine, nucleosides with 2-aminopurine bases, and the like, that may be employed. Conversely, a "mismatch" in a duplex between a targetpolynucleotide and an oligonucleotide probe or primer means that a pair of nucleotides in the duplex fails to undergo Watson-Crick bonding.
Oligonucleotide probes of the invention can be synthesized by a number of approaches, e.g. Ozaki et at, Nucleic Acids Research, 20:5205-5214 (1992); Agrawal et at, Nucleic Acids Research, 18:5419-5423 (1990); or the like. The oligonucleotideprobes of the invention are conveniently synthesized on an automated DNA synthesizer, e.g. an Applied Biosystems, Inc. Foster City, Calif.) model 392 or 394 DNA/RNA Synthesizer, using standard chemistries, such as phosphoramidite chemistry, e.g.disclosed in the following references: Beaucage and Iyer, Tetrahedron, 48:2223-2311 (1992); Molko et al, U.S. Pat. Nos. 4,980,460; Koster et al, U.S. Pat. No. 4,725,677; Caruthers et al, U.S. Pat. Nos. 4,415,732; 4,458,066; and 4,973,679; and thelike. Alternative chemistries, e.g. resulting in non-natural backbone groups, such as phosphorothioate, phosphoramidate, and the like, may also be employed provided that the hybridization efficiencies of the resulting oligonucleotides and/or cleavageefficiency of the exonuclease employed are not adversely affected. Preferably, theoligonucleotide probe is in the range of 15-60 nucleotides in length. More preferably, the oligonucleotide probe is in the range of 18-30 nucleotides in length. Theprecise sequence and length of an oligonucleotide probe of the invention depends in part on the nature of the target polynucleotide to which it binds. The binding location and length may be varied to achieve appropriate annealing and melting propertiesfor a particular embodiment. Preferably, the 3' terminal nucleotide of the oligonucleotide probe is blocked or rendered incapable of extension by a nucleic acid polymerase. Such blocking is conveniently carried out by the attachment of a reporter orquencher molecule to the terminal 3' carbon of the oligonucleotide probe by a linking moiety. Preferably, reporter molecules are fluorescent organic dyesderivatized for attachment to the terminal 3' carbon or terminal 5' carbon of the probe via alinking moiety. Preferably, quencher molecules are also organic dyes, which may or may not be fluorescent, depending on the embodiment of the invention. For example, in a preferred embodiment of the invention, the quencher molecule is fluorescent. Generally, whether the quencher molecule is fluorescent or simply releases the transferred energy from the reporter by non-radiative decay, the absorption band of the quencher should substantially overlap the fluorescent emission band of the reportermolecule. Non-fluorescent quencher molecules that absorb energy from excited reporter molecules, but which do not release the energy radiatively, are referred to herein as chromogenic molecules. There is a great deal of practical guidance available inthe literature for selecting appropriate reporter-quencher pairs for particular probes, as exemplified by the following references: Clegg "Fluorescence resonance energy transfer and nucleic acids," Methods of Ettzymology, 211:353-389 (1992), Wu et al;"Resonance energy transfer: methods and applications," Anal. Biochem. 218: 1-13 (1994).; Pesce et at, editors, Fluorescence Spectroscopy (Marcel Dekker, New York, 1971); White et at, Fluorescence Analysis: A Practical Approach (Marcel Dekker, New York,1970); and the like. The literature also includes references providing exhaustive lists of fluorescent and chromogenic molecules and their relevant optical properties for choosing reporter-quencher pairs, e.g. Berlman, Handbook of Fluorescence Sprectraof Aromatic Molecules, 2nd Edition (Academic Press, New York, 1971); Griffiths, Colour and Consitution of Organic Molecules (Academic Press, New York, 1976); Bishop, editor, Indicators (Pergamon Press, Oxford, 1972); Haugland, Handbook of FluorescentProbes and Research Chemicals (Molecular Probes, Eugene, 1992); Pringsheim, Fluorescence and Phosphorescence (Interscience Publishers, New York, 1949); and the like. Further, there is extensive guidance in the literature for derivatizing reporter andquencher molecules for covalent attachment via common reactive groups that can be added to an oligonucleotide, as exemplified by the following references: Haugland (cited above); Ullman et al, U.S. Pat. No. 3,996,345; Khanna et al, U.S. Pat. No.4,351,760; and the like.
Exemplary reporter-quencher pairs may be selected from xanthene dyes, including fluoresceins, and rhodamine dyes. Many suitable forms of these compounds are widely available commercially with substituents on their phenyl moieties which can beused as the site for bonding or as the bonding functionality for attachment to an oligonucleotide. Another group of fluorescent compounds are the naphthylamines, having an amino group in the alpha or beta position. Included among such naphthylaminocompounds are 1-dimethylaminonaphthyl-5-sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include 3-phenyl-7-isocyanatocoumarin, acridines, such as 9-isothiocyanatoacridine and acridine orange;N-(p-(2-benzoxazolyl)phenyl)malcimide; benzoxadiazoles, stilbenes, pyrenes, and the like. Preferably, reporter and quencher molecules are selected from fluorescein and rhodamine dyes. These dyes and appropriate linking methodologies for attachment tooligonucleotides are described in many references, e.g. Khanna et al (cited above); Marshall, Histochemical J., 7:299-303 (1975); Mechnen et at, U.S. Pat. No. 5,188,934; Menchen et al, European pat. No. application 87310256.0; and Bergot et al,International application PCT/US90/05565. The latter four documents are hereby incorporated by reference.
There are many linking moieties and methodologies for attaching reporter or quencher molecules to the 5' or 3' termini of oligonucleotides, as exemplified by the following references: Eckstein, editor, Oligonucleotides and Analogues: A PracticalApproach (IRL Press, Oxford, 1991); Zuckerman et al, Nucleic Acids Research, 15: 5305-5321 (1987)(3' thiol group on oligonucleotide); Sharma et al, Nucleic Acids Research, 19:3019 (1991)(3' sulfhydryl); Giusti et al, PCR Methods and Applications,2:223-227 (1993) and Fung et al, U.S. Pat. No. 4,757,141 (5' phosphoamino group via Aminolink. II available from Applied Biosystems, Foster City, Calif.); Stabinsky, U.S. Pat. No. 4,739,044 (3' aminoalkylphosphoryl group); Agrawal et al, TetrahedronLetters, 31:1543-1546 (1990)(attachment via phosphoramidate linkages); Sproat et al, Nucleic Acids Research, 15:4837 (1987)(5' mercapto group); Nelson et al, Nucleic Acids Research, 17:7187-7194 (1989)(3' amino group); and the like. Preferably,commercially available linking moieties are employed that can be attached to an oligonucleotide during synthesis, e.g. available from Clontech Laboratories (Palo Alto, Calif.).
Rhodamine and fluorescein dyes are also conveniently attached to the 5' hydroxyl of an oligonucleotide at the conclusion of solid phase synthesis by way of dyes derivatized with a phosphoramidite moiety, e.g. Woo et al, U.S. Pat. No.5,231,191; and Hobbs, Jr. U.S. Pat. No. 4,997,928.
The selection of primers and probes used in this invention is at the choice of the practitioner. This invention places no unique requirements or restrictions on primer or probe choice. Such choices are within the skill of the art.
The probes can be of any length, so long as that length allows one to practice the invention. As a baseline the longer probe must have at least 3 base pairs; as a practical matter the longer probe will be comprised of more than 3 base pairs. However, there is no upper limit occasioned by the use of FETCH. The length of the longer probe is not dictated by the application of FETCH as it will work with any length of probe, over and above the basic requirement of being at least 3 base pairslong. As a practical matter the longer probe will have a length which insures that it hybridizes uniquely with the target polynucleotide and the shorter probe. The shorter probe will be at least 2 fewer base pairs than that of the longer probe. Thisis the basic standard for creating the shorter probe. It has been found that a good fit as regards the difference in length between the probes can be arrived at by calculating the dissociation temperature of the annealed probes. As a general rule thedissociation temperature of the primers needs to be higher than about 55 degrees C. and lower than 90 degrees C. A convenient means for doing this calculation is to use the software called Gene Runner (Hastings Software, Inc.), for example version 3.04.
The shorter probe may be prepared as a 5' truncate of the longer probe. Or it may be a 3' truncate. A third option is to create the shorter probe by truncating both the 5' and the 3' end of the longer probe. Any one of these three forms ofthe shorter probe will work. While two or more truncated forms could be used, it is simplest to use just one form, preferably the 5' truncate form.
The fluorophore and the quencher can be located on any combination of base pairs so long as the fluorescence of the fluorophore is effectively quenched by the quencher when the two probes are hybridized. The simplest approach is to put thefluorophore on the 5' terminal nucleotide of the longer probe and the quencher on the 3' terminal nucleotide of the shorter probe. This approach can optimizes the quencher molecules affect on the fluorescence of the fluorophore. Preferably, fluorophoreand quencher molecules are attached to the terminal 5' carbon and terminal 3' carbon of the probe by way of 5' and 3' linking moieties. However it has been demonstrated that, with at least a number of the fluorophores useful herein, that the fluorophoreand the quencher can be situated remotely and still be operative. See for example U.S. Pat. No. 5,538,848 which discloses that a fluorophore and quencher may be separated by several nucleotides. That patent discloses work where a fluorophore andquencher are separated by at least 15 nucleotides, or more, and allegedly demonstrate utility. Likewise herein the fluorophore and quencher are permitted to be separated by numerous nucleotides, so long as that separation does not materially reduce theability of the quencher to affect the signal of the fluorophore when the two probes are hybridized. Of course the fluorophore and/or quencher could be bonded to a nucleotide in the interior of the probes. But for reasons of ease of synthesis and foroptimizing hybridization of probe to target and probe to probe, it is preferable to put the fluorophore and quencher on the 5' and 3' terminal ends of the probes, as noted above. In fact the fluorophore and quencher both be on the 5' or 3' terminalnucleotides of their respective oligonucleotides, and the assay will be functional. An alternative arrangement would be to put the fluorophore on the shorter probe and the quencher on the longer probe. Again in this arrangement the longer probe wouldpreferentially bind to the target and thus be separated sufficiently from the probe with the fluorophore so as not to effectively quench its fluorescence. The preferred construct, however, is to have the fluorophore on the longer probe.
The following examples are given to illustrate the invention and are not intended nor should they be read to limit the scope of the invention as claimed in any fashion.
The use of fluorescence energy transfer by competitive hybridization (FETCH) was developed as an assay for the detection by PCR of hepatitis C virus (HCV) in human specimens. The forward probe, the longer probe, had a 6-FAM dye(carboxyfluoroscein) at the 5' position and a phosphate group at the 3' position (to prevent extension during PCR). The reverse probe, the shorter probe, had a TAMRA dye (N,N,N',N' tetramethyl-6-carboxyrhodamine) at the 3' position (no 3' OH thus noextension possible during PCR). FAM, a commonly used fluorescent dye, was used as the fluorophore. TAMRA, a fluorescent dye with absorption band overlapping the emission band of FAM, was used as the quencher in this application
Selection of Primers and Probes
HCV polynucleotide sequences were identified from the literature. In order to have an assay which could catch all known HCV strains, two primers and two probes were selected which had polynucleotide sequences common to all reported strain RNAsequences. The primers were selected so that they would anneal to all the known HCV strains and possess satisfactory characteristics such as similar dissociation temperature, no extensive 3' complementarity to each other, etc. The ones chosen flank a254 bp segment of the 5' non-coding region of HCV from nucleotide number 3290 to 3543 (SEQ ID NO: 5) as described in the literature. The HCV sequence data relied on, the primers, and the selected probes are identified in the following Tables I-III(attached).
TABLE-US-00001 TABLE I Oligo Bases MW Label HCV Forward Primer Sequence 5'-GCGTTAGTATGAGTGTCGTGCAG 26 8008 None CCT-3' (SEQ ID NO: 1) HCVR2 Reverse Primer Sequence 5'-GGTGCACGGTCTACGAGACC-3' 20 6124 None (SEQ ID NO: 2)
TABLE-US-00002 TABLE II TARGET SEQUENCE 3331-3350 Probe C1 5'-FAM-CCGGGAGAGCCATAGTGGTC PO4 (SEQ ID NO: 3) Probe C2 3'-TAMRA-GGCCCTCTCGGTATCAC (SEQ ID NO: 4)
The unconventional presentation of the sequence of C2 (from 3' to 5') is to aid the visualization of its complementarity to C1.
TABLE-US-00003 TABLE III Bases MW Label Probe C1 20 6914 6-FAM Probe C2 17 6065 TAMRA
Molecular weights calculated by Gene Runer version 3.04 (Hastings Software, Inc.)
Synthesis of Probes
Two probes were custom-synthesized at TriLink Biotechnologies, Inc. (11585 Sorrento Valley Rd., Suite 105, San Diego, Calif. 92121) They were prepared as follows:
Step 1.: Synthesis of Oligonucleotide
The oligonucleotide was prepared on a support that will yield a 3' phosphate group upon deprotection (Glen Research Catalog No. 20-2913).
Step 2.: Addition of 6-FAM
The support bound oligonucleotide was then reacted with 15 eqs. of 6-FAM amidite (Glen Research Catalog No. 10-5901) manually to ensure high efficiency.
Step 3.: Deprotection of Oligonucleotide
The FAM labeled oligo was deprotected for 36 hours at room temperature with fresh conc. ammonium hydroxide. After deprotection the reagent was decanted, the beads rinsed, and the combined solutions dried.
Step 4.: Purification
The FAM labeled oligonucleotide was purified using reverse phase HPLC. The FAM was only on full length material, and was a useful lipophilic handle allowing good separation. After purification, the compound was dried down in preparation forprecipitation. The compound was precipitated from 0.3 M NaOAc using EtOH. The product was recovered by high speed centrifugation and washed twice with EtOH.
Step 5.: Final Analysis
The dried product was resuspended in water, quantitated, and analyzed by HPLC for purity. The compound was then dried again in preparation for delivery.
Detection of HCV RNA by Reverse Transcriptase-PCR Using Fetch
The assay was carried out as a one-step reverse transcription and polymerase chain reaction. HCV RNA was isolated and purified from human serum or plasma. The serum or plasma sample was lysed under highly denaturing conditions to inactivateRNAases and to insure isolation of intact RNA. The RNA was precipitated with ethanol and transferred to a QIAmp spin column (Qiagen, Chatsworth, Calif.) that binds RNA. The column was then washed and RNA eluted with water. The purified RNA template(10 L) was mixed with HCV master mix (see Table V) (40 L) and then reverse transcribed to DNA, amplified by PCR and detected in the same tube in the Perkin Elmer 7700 sequence analyzer as per Table VI. During PCR, some of the FAM labeled probe and someof the TAMRA labeled probe annealed to the PCR product thus reducing the quenching of FAM fluorescence and allowed increased fluorescence to be detected. The fluorescence of FAM increase with increasing number of cycles of thermocycling, correspondingwith increases in amount of PCR product, as illustrated in FIG. 1.
TABLE-US-00004 TABLE IV Typical HCV Master Mix 1 Tube Final conc. Reagents (μL) (40 μL) Water RNase Free 26.8 -- X TaqMan ™ Buffer 5 1X MgCl2 (25 mM) 5 2.5 mM dNTP5 (25 mM each) 0.6 300 μM Primer HCVC1 (100 μM) 0.25 500nM Primer HCVC2 (100 μM) 0.25 500 nM Probe C1 (25 μM) 0.2 100 nM Probe C2 (25 μM) 0.2 100 nM RNase Inhibitor (20 U/μL) 0.5 10 U MU/V RT (50 U/μL) 0.5 25 U Amplitaq Gold (5 U/μL) 0.5 2.5 U TaqMan ™ is the trademark of Roche MolecularSystems, Inc.
TABLE-US-00005 TABLE V Auto Cycle Temperature Time Repeat Ramp Time Increment Hold 48 degrees 60:00 Auto Hold 95 degrees 10:00 Auto Cycle 93 degrees 0:15 40 Auto 57 degrees 0:30 72 degrees 0:30
TABLE-US-00006 TABLE VI SEQ ID NO: 5 ##STR00001##
5epatitis C virus gtat gagtgtcgtg cagcct 2622atitis C virus 2ggtgcacggt ctacgagacc 2Hepatitis C virus 3ccgggagagc catagtggtc2Hepatitis C virus 4cactatggct ctcccgg NAHepatitis C virus 5actcccctgt gaggaactac tgtcttcacg cagaaagcgt ctagccatgg cgttagtatg 6gtgc agcctccagg accccccctc ccgggagagc catagtggtc tgcggaaccg gtacac cggaattgcc aggacgaccg ggtcctttcttggataaacc cgctcaatgc agattt gggcgtgccc ccgcaagact gctagccgag tagtgttggg tcgcgaaagg 24ggta ctgcctgata gggtgcttgc gagtgccccg ggaggtctcg tagaccgtgc 3gagca cgaatcctaa acctcaaaga aaaaccaaac gtaacaccaa ccgtcgccca 36
Field of SearchInvolving nucleic acid
Polynucleotide (e.g., nucleic acid, oligonucleotide, etc.)
Acellular exponential or geometric amplification (e.g., PCR, etc.)
Probes for detection of specific nucleotide sequences or primers for the synthesis of DNA or RNA
Labels or markers utilized (e.g., radiotracer, affinity, fluoroescent, phosphorescent, markers, etc.)